Coentrao, who has been one of Benfica's best performers in the Champions' League this season, injured his right knee during the 4-0 win against Naval on Sunday.
Varela, who has scored six goals to help Porto earn a 10-point lead in the Portuguese Premier League, had to be replaced in the first of half of his team's victory against Portimonense after picking up a thigh injury.
Coach Paulo Bento has called up Toulouse midfielder Paulo Machado and Genoa's Miguel Veloso, a midfielder who can also play at left-back, to replace the duo, the FPF added in a statement.
The friendly is being held as part of the effort to promote the joint bid by the two countries to host the 2018 World Cup, with FIFA's decision due on December 2.
The match in Lisbon is also an opportunity for Portugal to avenge their World Cup last-16 defeat to the Spanish.
Portugal squad:
Goalkeepers: Eduardo (Genoa), Rui Patricio (Sporting)
Defenders: Bruno Alves (Zenit St. Petersburg), Jose Bosingwa (Chelsea), Joao Pereira (Sporting), Pepe (Real Madrid), Ricardo Carvalho (Real Madrid).
Midfielders: Carlos Martins (Benfica), Joao Moutinho (Porto), Manuel Fernandes (Valencia), Miguel Veloso (Genoa), Paulo Machado (Toulouse FC) e Raul Meireles (Liverpool).
Forwards: Cristiano Ronaldo (Real Madrid), Danny (Zenit St. Petersburg), Helder Postiga (Sporting), Hugo Almeida (Werder Bremen), Nani (Manchester United).
